Release NotesRelease 10.0, Tuesday April 26th 2005
R.Apweiler (1), T.K.Attwood (4), A.Bairoch (2), A.Bateman (5), D.Binns (1), P.Bork (8), P.Bucher (3), M.J.Campbell (14), L.Cerutti (3), R.Copley (13), E.Courcelle (6), U.Das (1), L.Daugherty (1), M.Dibley (7), R.Durbin (5), W.Fleischmann (1), J.Gough (11), D.Haft (9), N.Hulo (2), S.Hunter (1), D.Kahn (6), A.Kanapin (1), M.Krestyaninova (1), D.Lonsdale (1), R.Lopez (1), I.Letunic (8), M.Madera (12), J.Maslen (1), J.McDowall (1), J.Mistry (5), A.Mitchell (1,4), N.Mulder (1), A.N.Nikolskaya (10), S.Orchard (1), C.Orengo (7), M.Pagni (3), D.Peyruc (6), E.Quevillon (1), C.Sigrist (2), V.Silventoinen (1), P.D.Thomas (14), R.Vaughan (1), C.H.Wu (10).
(1) EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK;
(2) Swiss Institute for Bioinformatics, Geneva, Switzerland;
(3) Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland;
(4) School of Biological Sciences, The University of Manchester, Manchester, UK;
(5) The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK;
(6) CNRS/INRA, Toulouse, France;
(7) Biochemistry and Molecular Biology Department, University College London, University of London, UK;
(8) Biocomputing Unit, EMBL-Heidelberg, Germany;
(9) The Institute for Genomic Research, Maryland, USA;
(10) Protein Information Resource, Georgetown University Medical Center, Washington, D.C., USA;
(11) Genomic Sciences Centre, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Japan;
(12) MRC Laboratory of Molecular Biology, Cambridge, UK;
(13) Wellcome Trust Centre for Human Genetics, Oxford, UK;
(14) Computational Biology, Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA.
The databases UniProt, PROSITE, PRINTS, Pfam, and ProDom joined forces to launch an Integrated Documentation Resource of Protein Families, Domains and Functional Sites, abbreviated InterPro. Since then SMART, TIGRFAMs, PIRSF, SUPERFAMILY, and more recently PANTHER and Gene3D, have joined InterPro. A detailed description of the project can be found in the user manual.
This release marks the 5th anniversary of InterPro, a brief history of the database and the milestones in its development are outlined in "History and Development".
Changes since last release
Protein matches have been updated according to the latest update of UniProt and new methods from Gene3D, PANTHER, Pfam, PIRSF, PROSITE and TIGRFAMs, have been integrated.
InterPro entries have a new webpage design:
- Relationships between entries are now featured diagrammatically in a new section, 'Overlapping InterPro entries'. Where the InterPro entry shares more than 70% of proteins with other InterPro entries, the numbers of non-overlapping and overlapping proteins between the entries is displayed in a Venn diagram. For Domain overlaps, the average overlap in amino acids, of the protein signatures for each protein is then calculated and the results displayed as a bar diagram; this diagram is only shown for 'Domain - Domain' protein signature overlaps.
- Section headers are linked directly to the user manual.
- The section providing information on the Dates an entry was created and subsequently modified has been discontinued.
A new version of InterProScan is available; InterPro matches and matches to GO terms can be displayed and InterPro results can be filtered by taxonomy.
Contents and coverage of the current release
InterPro protein matches are now calculated for all UniProt proteins, which are a combination of UniProt/Swiss-Prot, UniProt/TrEMBL and PIR proteins. For more information see UniProt.
InterPro release 10.0 contains 11972 entries, representing 3079 domains, 8597 families, 228 repeats, 27 active sites, 21 binding sites and 20 post-translational modification sites. Overall, there are 7521179 InterPro hits from 1466570 UniProt protein sequences. A complete list is available from the ftp site.
91.8% of UniProt/Swiss-Prot - 165778 of 180652 proteins
77.0% of UniProt/TrEMBL - 1300792 of 1689375 proteins
78.4% of UniProt - 1466570 of 1870027 proteins
Last entry: IPR012680
19604 publications in PUBMED are referenced from InterPro.
The next release of InterPro will be release 10.1 scheduled for July 2005. It will incorporate:
- Links to MODBASE
- Improvements to the taxonomy, more detailed taxonomy and FASTA downloads
- Additional reading, linked to abstracts
- InterPro classification heirarchy based on GO terms